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- PDB-7exy: T-hairpin structure found in the RNA element involved in the piRN... -

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Entry
Database: PDB / ID: 7exy
TitleT-hairpin structure found in the RNA element involved in the piRNA biogenesis
ComponentsRNA (5'-R(*UP*UP*GP*GP*UP*UP*UP*GP*AP*UP*UP*CP*CP*AP*AP*G)-3')
KeywordsRNA / piRNA / cis element
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
AuthorsTakase, N. / Kawai, G.
CitationJournal: Rna / Year: 2022
Title: T-hairpin structure found in the RNA element involved in piRNA biogenesis.
Authors: Takase, N. / Otsu, M. / Hirakata, S. / Ishizu, H. / Siomi, M.C. / Kawai, G.
History
DepositionMay 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*UP*UP*GP*GP*UP*UP*UP*GP*AP*UP*UP*CP*CP*AP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,0771
Polymers5,0771
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: RNA chain RNA (5'-R(*UP*UP*GP*GP*UP*UP*UP*GP*AP*UP*UP*CP*CP*AP*AP*G)-3')


Mass: 5077.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H HOHAHA

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Sample preparation

DetailsType: solution
Contents: 0.3 mM None RNA (5'-R(*UP*UP*GP*GP*UP*UP*UP*GP*AP*UP*UP*CP*CP*AP*AP*G)-3'), 95% H2O/5% D2O
Label: tj-17-32 / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.3 mM
Component: RNA (5'-R(*UP*UP*GP*GP*UP*UP*UP*GP*AP*UP*UP*CP*CP*AP*AP*G)-3')
Isotopic labeling: None
Sample conditionsDetails: 20 mM sodium phosphate buffer (pH 6.5) with 50 mM NaCl
Ionic strength: 50 mM / Label: tj-17-32 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.114Goddardchemical shift assignment
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
Sparky3.114Goddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 11

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